DataAnalysis - Postprocessing Results MaxQuant

1 Global Parameters

###############################
#
#define settings
#
###############################

GET_SAMPLE_NAMES <- TRUE # if set to FALSE define it in the next line
#sample_names_user <- c()

unique <- params$unique  # how many peptides should be at least necessary to identify a protein


# which types should be evaluated TRUE or FALSE could be used
RAZOR <- FALSE
UNIQUE <- FALSE
LFQ <- FALSE
if (any(grepl("RAZOR",params$protein_types))){
  RAZOR <- TRUE
}
if (any(grepl("UNIQUE",params$protein_types))){
  UNIQUE <- TRUE
}
if (any(grepl("LFQ",params$protein_types))){
  LFQ <- TRUE
}

# define path of the proteinGroups.txt file(s)
path = params$path

# save files | options
# FALSE - results are not saved
# "RDS" - save results into R data file format
# "CSV" - save results into a csv file
SAVE <- "FALSE"
if (any(grepl("RDS",params$SAVE))){
  SAVE <- "RDS"
}
if (any(grepl("CSV",params$SAVE))){
  SAVE <- "CSV"
}

2 Introduction

2.1 Unique | Razor&Unique procedure

Filtering:

• Potential.contaminant != "+" -> remove where contaminants

• Reverse != "+"-> remove where reverse = +

• Only.identified.by.site != "+" -> remove where only identified by site = +

• data[name] >= unique -> keep only identifications which have greater or equal number (defined via variable unique) of razor/unique peptides | typically this is set to 1 or 2

Data analysis show the number of identified proteins and the heatmap. In Summary the final results are visualized as boxplot and a table with the summarized values is shown.

2.2 LFQ-Procedure

Filtering:

• Potential.contaminant != "+" -> remove where contaminants = +
• Reverse != "+"-> remove where reverse = +
• Only.identified.by.site != "+" -> remove where only identified by site = +

Then the log2of the LFQ intensities is calculated and all -Inf values were substituted by NA using the following command: lfq[lfq == -Inf] <- NA

Data analysis show the number of identified proteins and the heatmap. In Summary the final results are visualized as boxplot and a table with the summarized values is shown.

3 Load required packages and functions

# load libraries
library(tidyverse)
library(dplyr)
library(pheatmap)
library(ggplot2)
library(reshape2)
library(plotly)
library(knitr)
# load functions
source("filtering_function.R")
print("loading sucessful")

## [1] "loading sucessful"

4 Data Analysis

The txt-files of the defined folder are read in, processed and filtered automatically. This section shows the code, heatmaps for LFQ values and also some summary statistics.

########## read in all data with pattern .txt
# get file list
file.list <- list.files(path = path, pattern='*.txt')
# create file path
file.path <- paste(path,file.list,sep = "")
# read in files - for each file one variable is created - results are stored in a list
res_raw <- lapply(file.path, read.delim)
names(res_raw) <- file.list

########## get sample names
if (GET_SAMPLE_NAMES == TRUE){
  #get sample names
  tmp <- colnames(res_raw[[1]])
  tmp <- tmp[grep("Razor...unique.peptides.",tmp)]
  tmp <- sub(".*Razor...unique.peptides.", "",tmp)
  sample_names_raw <- tmp
  rm(tmp)
  #create sample names
  sample_names_razor <- paste("Razor...unique.peptides.",sample_names_raw, sep="")
  sample_names_unique <- paste("Unique.peptides.",sample_names_raw, sep="")
  sample_names_lfq <- paste("LFQ.intensity.",sample_names_raw, sep="")
} else {
  for (i in 1:length(file.list)){
    # rename columns
    res_raw[[i]] <- res_raw[[i]] %>%
       rename_with(~ paste("Razor_", sample_names_user, sep = ""),
                   starts_with("Razor...unique.peptides.")) %>%
       rename_with(~ paste("Unique_", sample_names_user, sep = ""),
                   starts_with("Unique.peptides.")) %>%
       rename_with(~ paste("LFQ_", sample_names_user, sep = ""),
                   starts_with("LFQ.intensity."))
    # get column names
    sample_names_razor <- colnames(res_raw[[i]][grep("Razor_",
                                                colnames(res_raw[[i]]))])
    sample_names_unique <- colnames(res_raw[[i]][grep("Unique_",
                                                colnames(res_raw[[i]]))])
    sample_names_lfq <- colnames(res_raw[[i]][grep("LFQ_",
                                                 colnames(res_raw[[i]]))])
    }
}

########## create result data frame & result lists
# create data frame for razor
results_2gether_razor <- data.frame(matrix(ncol = length(sample_names_razor), nrow = length(file.list)))
row.names(results_2gether_razor) <- file.list
colnames(results_2gether_razor) <- sample_names_razor
#create data frame for unique
results_2gether_unique <- data.frame(matrix(ncol = length(sample_names_unique), nrow = length(file.list)))
row.names(results_2gether_unique) <- file.list
colnames(results_2gether_unique) <- sample_names_unique
#create data frame for lfq
results_2gether_lfq <- data.frame(matrix(ncol = length(sample_names_lfq), nrow = length(file.list)))
row.names(results_2gether_lfq) <- file.list
colnames(results_2gether_lfq) <- sample_names_lfq

#results lists
results_razor <- list()
results_unique <- list()
results_lfq <- list()

########## perform evaluation
if (RAZOR == TRUE) {
  cat("\n")
  cat("##","Razor","\n")
  cat("\n")
  for (x in file.list){
    cat("\n")
    cat("###",substring(x, 1, nchar(x)-4),"\n")
    data_raw <- as.data.frame(res_raw[[x]])
    data <- filtering(data_raw)
    fasta <- data$Fasta.headers
    results <- data.frame(matrix(ncol = length(sample_names_razor), nrow = nrow(data)))
    colnames(results) <- sample_names_razor
    i <- 0
    for (i in 1:length(sample_names_razor)){
      name <- sample_names_razor[i]
      tmp <- (data[name] >= unique)
      results[i] <- tmp
      cat(name,"<br/>",sum(tmp, na.rm = TRUE),"<br/>")
    }
    results_razor[[x]] <- results
    results_2gether_razor[x,] <- sapply(results,function(x)sum(x, na.rm = TRUE))
    cat("\n")
    
        #create heatmaps
    paletteLength <- 2
    myColor <- colorRampPalette(c("navy", "white",
                                  "firebrick3"))(paletteLength)
      data4pheatmap <- results
      data4pheatmap <- results
      data4pheatmap <- data4pheatmap*1
      data4pheatmap[data4pheatmap == 0] <- NA
      # remove NA rows
      ind <- apply(data4pheatmap, 1, function(x) all(is.na(x)))
      data4pheatmap_clear <- data4pheatmap[!ind,]
      data4pheatmap_clear[is.na(data4pheatmap_clear)] <- 0
      if (ncol(data4pheatmap_clear) < 2){
        cat("\n")
        cat("##"," No heatmap possible. Too less columns in the result
            table.","\n")
      } else {
        pheatmap(data4pheatmap_clear,
                 legend_breaks = c(0,1),
                 color = myColor,
                 treeheight_row = 10,
                 angle_col ="45",
                 treeheight_col = 10,
                 legend = TRUE,
                 labels_row = rep("",nrow(data4pheatmap)),
                 labels_col = sample_names_raw)
        cat("\n")
      }
  }
}

4.1 Razor

4.1.1 proteinGroups

## Warning: `summarise_each_()` was deprecated in dplyr 0.7.0.
## ℹ Please use `across()` instead.
## ℹ The deprecated feature was likely used in the dplyr package.
##   Please report the issue at <]8;;https://github.com/tidyverse/dplyr/issueshttps://github.com/tidyverse/dplyr/issues]8;;>.

## Warning: `funs()` was deprecated in dplyr 0.8.0.
## ℹ Please use a list of either functions or lambdas:
## 
## # Simple named list: list(mean = mean, median = median)
## 
## # Auto named with `tibble::lst()`: tibble::lst(mean, median)
## 
## # Using lambdas list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))

[1] “!NA values detected!” Only.identified.by.site 1 133 Razor…unique.peptides.a1
9
Razor…unique.peptides.a2
18
Razor…unique.peptides.a3
16
Razor…unique.peptides.a4
24
Razor…unique.peptides.a5
29
Razor…unique.peptides.a6
25
Razor…unique.peptides.a7
21
Razor…unique.peptides.b1
9
Razor…unique.peptides.b2
9
Razor…unique.peptides.b3
9
Razor…unique.peptides.b4
10
Razor…unique.peptides.b5
13
Razor…unique.peptides.b6
4
Razor…unique.peptides.b7
8

if (UNIQUE == TRUE) {
  cat("\n")
  cat("##","Unique","\n")
  cat("\n")
  for (x in file.list){
    cat("\n")
    cat("###",substring(x, 1, nchar(x)-4),"\n")
    data_raw <- as.data.frame(res_raw[[x]])
    data <- filtering(data_raw)
    results <- data.frame(matrix(ncol = length(sample_names_unique), nrow = nrow(data)))
    colnames(results) <- sample_names_unique
    i <- 0
    for (i in 1:length(sample_names_unique)){
      name <- sample_names_unique[i]
      tmp <- (data[name] >= unique)
      results[i] <- tmp
      cat(name,"<br/>",sum(tmp, na.rm = TRUE),"<br/>")
    }
    results_unique[[x]] <- results
    results_2gether_unique[x,] <- sapply(results,function(x)sum(x, na.rm = TRUE))
    cat("\n")
    #create heatmaps
    paletteLength <- 2
    myColor <- colorRampPalette(c("navy", "white",
                                  "firebrick3"))(paletteLength)
      data4pheatmap <- results
      data4pheatmap <- data4pheatmap*1
      data4pheatmap[data4pheatmap == 0] <- NA
      # remove NA rows
      ind <- apply(data4pheatmap, 1, function(x) all(is.na(x)))
      data4pheatmap_clear <- data4pheatmap[!ind,]
      data4pheatmap_clear[is.na(data4pheatmap_clear)] <- 0
      if (ncol(data4pheatmap) < 2){
        cat("\n")
        cat("##"," No heatmap possible. Too less columns in the result
            table.","\n")
      } else {
        pheatmap(data4pheatmap_clear,
                 legend_breaks = c(0,1),
                 color = myColor,
                 treeheight_row = 10,
                 angle_col ="45",
                 treeheight_col = 10,
                 legend = TRUE,
                 labels_row = rep("",nrow(data4pheatmap)),
                 labels_col = sample_names_raw)
        cat("\n")
      }
  }
}

4.2 Unique

4.2.1 proteinGroups

[1] “!NA values detected!” Only.identified.by.site 1 133 Unique.peptides.a1
9
Unique.peptides.a2
17
Unique.peptides.a3
15
Unique.peptides.a4
24
Unique.peptides.a5
28
Unique.peptides.a6
24
Unique.peptides.a7
20
Unique.peptides.b1
8
Unique.peptides.b2
7
Unique.peptides.b3
8
Unique.peptides.b4
9
Unique.peptides.b5
12
Unique.peptides.b6
4
Unique.peptides.b7
8

if (LFQ == TRUE) {
  cat("\n")
  cat("##","LFQ","\n")
  cat("\n")
  for (x in file.list){
    cat("\n")
    cat("###",substring(x, 1, nchar(x)-4),"\n")
    data_raw <- as.data.frame(res_raw[[x]])
    data <- filtering(data_raw)
    
    results <- data.frame(matrix(ncol = length(sample_names_lfq), nrow = nrow(data)))
    colnames(results) <- sample_names_lfq
    i <- 0
    for (i in 1:length(sample_names_lfq)){
      name <- sample_names_lfq[i]
      tmp <- log2(data[name])
      tmp[tmp == -Inf] <- NA
      results[i] <- tmp
      cat(name,"<br/>",sum(!is.na(tmp)),"<br/>")
      
    }
    
    results_lfq[[x]] <- results
    results_2gether_lfq[x,] <- sapply(results,function(x)sum(!is.na(x)))
    cat("\n")
    
    #create heatmaps
    paletteLength <- 50
    myColor <- colorRampPalette(c("navy", "white",
                                  "firebrick3"))(paletteLength)
      data4pheatmap <- results
      data4pheatmap <- results
      data4pheatmap <- data4pheatmap*1
      data4pheatmap[data4pheatmap == 0] <- NA
      # remove NA rows
      ind <- apply(data4pheatmap, 1, function(x) all(is.na(x)))
      data4pheatmap_clear <- data4pheatmap[!ind,]
      data4pheatmap_clear[is.na(data4pheatmap_clear)] <- 0
      if (ncol(data4pheatmap) < 2){
        cat("\n")
        cat("##"," No heatmap possible. Too less columns in the result
            table.","\n")
      } else {
        pheatmap(data4pheatmap_clear,
                 color = myColor,
                 treeheight_row = 10,
                 angle_col ="45",
                 treeheight_col = 10,
                 legend = TRUE,
                 labels_row = rep("",nrow(data4pheatmap)),
                 labels_col = sample_names_raw)
        cat("\n")
      }
  }
}

5 Summary

# show summary
if (RAZOR == TRUE){
  cat("\n")
  cat("##"," Summary Razor","\n")
  print(kable(results_2gether_razor))
  
  ggplot(melt(results_2gether_razor),aes(x = variable, y = value)) +
  geom_boxplot() + 
  xlab("Sample name") + 
  scale_x_discrete(labels = sample_names_raw) +
  theme(axis.text.x = element_text(angle = 90)) +
  labs(title = "Razor")
}

5.1 Summary Razor

	Razor…unique.peptides.a1	Razor…unique.peptides.a2	Razor…unique.peptides.a3	Razor…unique.peptides.a4	Razor…unique.peptides.a5	Razor…unique.peptides.a6	Razor…unique.peptides.a7	Razor…unique.peptides.b1	Razor…unique.peptides.b2	Razor…unique.peptides.b3	Razor…unique.peptides.b4	Razor…unique.peptides.b5	Razor…unique.peptides.b6	Razor…unique.peptides.b7
proteinGroups.txt	9	18	16	24	29	25	21	9	9	9	10	13	4	8

if (UNIQUE == TRUE){
  cat("\n")
  cat("##"," Summary Unique","\n")
  print(kable(results_2gether_unique))
  
  ggplot(melt(results_2gether_unique),aes(x = variable, y = value)) +
  geom_boxplot() + 
  xlab("Sample name") + 
  scale_x_discrete(labels = sample_names_raw) +
  theme(axis.text.x = element_text(angle = 90)) +
  labs(title = "Unique")
}

5.2 Summary Unique

	Unique.peptides.a1	Unique.peptides.a2	Unique.peptides.a3	Unique.peptides.a4	Unique.peptides.a5	Unique.peptides.a6	Unique.peptides.a7	Unique.peptides.b1	Unique.peptides.b2	Unique.peptides.b3	Unique.peptides.b4	Unique.peptides.b5	Unique.peptides.b6	Unique.peptides.b7
proteinGroups.txt	9	17	15	24	28	24	20	8	7	8	9	12	4	8

if (LFQ == TRUE){
  cat("\n")
  cat("##"," Summary LFQ","\n")
  print(kable(results_2gether_lfq))
  
  ggplot(melt(results_2gether_lfq),aes(x = variable, y = value)) +
  geom_boxplot() + 
  xlab("Sample name") + 
  scale_x_discrete(labels = sample_names_raw) +
  theme(axis.text.x = element_text(angle = 90)) +
  labs(title = "LFQ")
}

# save results
results_final <- data.frame(results_2gether_razor,results_2gether_unique,results_2gether_lfq)
# get rid of NA columns
results_final <- results_final[,colSums(is.na(results_final))<nrow(results_final)]
if (SAVE == "RDS"){
  saveRDS(results_final, "./results_final.RDS")
} else if (SAVE == "CSV") {
  write.csv2(results_final, "./results_final.csv")
} 

6 Which proteins are in the blanks?

• used Razor petides and at least 2 peptides for identification

p <-  ggplot(melt(results_2gether_razor),aes(x = variable, y = value)) +
  geom_boxplot() + 
  xlab("Sample name") + 
  scale_x_discrete(labels = sample_names_raw) +
  theme(axis.text.x = element_text(angle = 90)) +
  labs(title = "Razor")
ggplotly(p)

dat <- results_razor[[1]]
dat$fasta <- fasta
human <- grep("HUMAN",dat$fasta)
trica <- grep("TRICA",dat$fasta)
# write human oder trica in a column
for (i in 1:nrow(dat)){
  if (grepl("HUMAN",dat$fasta[i])){
    dat$org[i] <- "HUMAN"
  }
  else if (grepl("TRICA",dat$fasta[i])){
    dat$org[i] <- "TRICA"
  }
  else {
    dat$org[i] <- NA
  }
}

dat$org[intersect(human,trica)] <- "HUMAN/TRICA"

dat4plot <- dat[,-c(ncol(dat)-1)]
dat4plot_long <- melt(dat4plot, id = c("org"))
tmp <- regmatches(dat4plot_long$variable,gregexpr("(?<=des.).*",dat4plot_long$variable,perl=TRUE))
tmp <- unlist(tmp)
dat4plot_long$variable <- tmp

p <- ggplot(data=dat4plot_long, aes(x=variable, y=as.numeric(value), fill=org)) +
  stat_summary(fun.y = sum, geom = "bar", position = "dodge") +
  xlab("sample name") +
  ylab("counts")
ggplotly(p)

for (i in 1:(ncol(dat)-2)){
  cat("\n")
  text <- paste(" Fasta Headers - Sample",sample_names_raw[i])
  cat("##",text,"\n")
  cat("\"n")
  print(dat$fasta[which(dat[,i])])
}

6.1 Fasta Headers - Sample a1

“n[1]”tr|A0A0C4DGN4|A0A0C4DGN4_HUMAN Zymogen granule protein 16 homolog B OS=Homo sapiens OX=9606 GN=ZG16B PE=1 SV=1;sp|Q96DA0|ZG16B_HUMAN Zymogen granule protein 16 homolog B OS=Homo sapiens OX=9606 GN=ZG16B PE=1 SV=3”
[2] “tr|A0A286YEY1|A0A286YEY1_HUMAN Immunoglobulin heavy constant alpha 1 (Fragment) OS=Homo sapiens OX=9606 GN=IGHA1 PE=1 SV=1;sp|P01876|IGHA1_HUMAN Immunoglobulin heavy constant alpha 1 OS=Homo sapiens OX=9606 GN=IGHA1 PE=1 SV=2;tr|A0A0G2JMB2|A0A0G2JMB2_HUMAN” [3] “sp|P01037|CYTN_HUMAN Cystatin-SN OS=Homo sapiens OX=9606 GN=CST1 PE=1 SV=3;sp|P01036|CYTS_HUMAN Cystatin-S OS=Homo sapiens OX=9606 GN=CST4 PE=1 SV=3”
[4] “sp|P01833|PIGR_HUMAN Polymeric immunoglobulin receptor OS=Homo sapiens OX=9606 GN=PIGR PE=1 SV=4”
[5] “sp|P02814|SMR3B_HUMAN Submaxillary gland androgen-regulated protein 3B OS=Homo sapiens OX=9606 GN=SMR3B PE=1 SV=2”
[6] “sp|P04080|CYTB_HUMAN Cystatin-B OS=Homo sapiens OX=9606 GN=CSTB PE=1 SV=2;tr|A0A1W2PS52|A0A1W2PS52_HUMAN Cystatin-B OS=Homo sapiens OX=9606 GN=CSTB PE=1 SV=1”
[7] “sp|P0DUB6|AMY1A_HUMAN Alpha-amylase 1A OS=Homo sapiens OX=9606 GN=AMY1A PE=1 SV=1;sp|P0DTE8|AMY1C_HUMAN Alpha-amylase 1C OS=Homo sapiens OX=9606 GN=AMY1C PE=1 SV=1;sp|P0DTE7|AMY1B_HUMAN Alpha-amylase 1B OS=Homo sapiens OX=9606 GN=AMY1B PE=1 SV=1;sp|P19961|” [8] “sp|P12273|PIP_HUMAN Prolactin-inducible protein OS=Homo sapiens OX=9606 GN=PIP PE=1 SV=1”
[9] “sp|Q96DR5|BPIA2_HUMAN BPI fold-containing family A member 2 OS=Homo sapiens OX=9606 GN=BPIFA2 PE=1 SV=2”

6.2 Fasta Headers - Sample a2

“n [1]”tr|A0A0C4DGN4|A0A0C4DGN4_HUMAN Zymogen granule protein 16 homolog B OS=Homo sapiens OX=9606 GN=ZG16B PE=1 SV=1;sp|Q96DA0|ZG16B_HUMAN Zymogen granule protein 16 homolog B OS=Homo sapiens OX=9606 GN=ZG16B PE=1 SV=3”
[2] “tr|A0A139WGR3|A0A139WGR3_TRICA Apolipophorins-like protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034740 PE=4 SV=1”
[3] “tr|A0A139WNV6|A0A139WNV6_TRICA Elongation factor 1-alpha 1-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC031771 PE=3 SV=1;tr|A0A7I2V3H3|A0A7I2V3H3_HUMAN Elongation factor 1-alpha OS=Homo sapiens OX=9606 GN=EEF1A1 PE=1 SV=1;tr|A0A7I2V659|A0A7I2V6” [4] “tr|A0A139WNX9|A0A139WNX9_TRICA Arginine kinase OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC030882 PE=2 SV=1”
[5] “tr|D2A4R3|D2A4R3_TRICA ATP synthase subunit beta OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC015322 PE=3 SV=1”
[6] “tr|D6W6D2|D6W6D2_TRICA Fatty acid synthase-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC011522 PE=4 SV=1”
[7] “tr|D6W849|D6W849_TRICA Transketolase-like protein 2 OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC004789 PE=4 SV=1”
[8] “tr|D6WF19|D6WF19_TRICA Actin-87E-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC003326 PE=3 SV=1”
[9] “tr|D6WJX6|D6WJX6_TRICA Vitellogenin domain-containing protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC013741 PE=4 SV=1”
[10] “tr|D6WSV2|D6WSV2_TRICA Tubulin beta chain OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC009589 PE=3 SV=1;tr|Q5ST81|Q5ST81_HUMAN Tubulin beta chain OS=Homo sapiens OX=9606 GN=TUBB PE=1 SV=1;tr|Q5JP53|Q5JP53_HUMAN Tubulin beta chain OS=Homo sapiens OX=9606 GN=” [11] “tr|D6WUQ7|D6WUQ7_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005377 PE=4 SV=2”
[12] “tr|D6WUQ8|D6WUQ8_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005376 PE=4 SV=1”
[13] “tr|D6WUQ9|D6WUQ9_TRICA Larval serum protein 1 gamma chain-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC006769 PE=4 SV=1”
[14] “tr|D6WV03|D6WV03_TRICA Glyceraldehyde-3-phosphate dehydrogenase OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC006170 PE=3 SV=1”
[15] “tr|D6X0M8|D6X0M8_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012178 PE=4 SV=1”
[16] “sp|P01833|PIGR_HUMAN Polymeric immunoglobulin receptor OS=Homo sapiens OX=9606 GN=PIGR PE=1 SV=4”
[17] “sp|P0DUB6|AMY1A_HUMAN Alpha-amylase 1A OS=Homo sapiens OX=9606 GN=AMY1A PE=1 SV=1;sp|P0DTE8|AMY1C_HUMAN Alpha-amylase 1C OS=Homo sapiens OX=9606 GN=AMY1C PE=1 SV=1;sp|P0DTE7|AMY1B_HUMAN Alpha-amylase 1B OS=Homo sapiens OX=9606 GN=AMY1B PE=1 SV=1;sp|P19961|” [18] “sp|P12273|PIP_HUMAN Prolactin-inducible protein OS=Homo sapiens OX=9606 GN=PIP PE=1 SV=1”

6.3 Fasta Headers - Sample a3

“n [1]”tr|A0A0C4DGN4|A0A0C4DGN4_HUMAN Zymogen granule protein 16 homolog B OS=Homo sapiens OX=9606 GN=ZG16B PE=1 SV=1;sp|Q96DA0|ZG16B_HUMAN Zymogen granule protein 16 homolog B OS=Homo sapiens OX=9606 GN=ZG16B PE=1 SV=3”
[2] “tr|A0A139WAN8|A0A139WAN8_TRICA Tropomyosin-1, isoforms 9A/A/B-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC031441 PE=3 SV=1;tr|A0A139WAL9|A0A139WAL9_TRICA Tropomyosin-1, isoforms 9A/A/B-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC0” [3] “tr|A0A139WAP9|A0A139WAP9_TRICA Tropomyosin-2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC011461 PE=3 SV=1”
[4] “tr|A0A139WGR3|A0A139WGR3_TRICA Apolipophorins-like protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034740 PE=4 SV=1”
[5] “tr|A0A139WNX9|A0A139WNX9_TRICA Arginine kinase OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC030882 PE=2 SV=1”
[6] “tr|D6W849|D6W849_TRICA Transketolase-like protein 2 OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC004789 PE=4 SV=1”
[7] “tr|D6WF19|D6WF19_TRICA Actin-87E-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC003326 PE=3 SV=1”
[8] “tr|D6WJX6|D6WJX6_TRICA Vitellogenin domain-containing protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC013741 PE=4 SV=1”
[9] “tr|D6WQ50|D6WQ50_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC009873 PE=4 SV=1”
[10] “tr|D6WUQ7|D6WUQ7_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005377 PE=4 SV=2”
[11] “tr|D6WUQ8|D6WUQ8_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005376 PE=4 SV=1”
[12] “tr|D6WUQ9|D6WUQ9_TRICA Larval serum protein 1 gamma chain-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC006769 PE=4 SV=1”
[13] “tr|D6X073|D6X073_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1;tr|A0A139WC75|A0A139WC75_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1”
[14] “sp|P01833|PIGR_HUMAN Polymeric immunoglobulin receptor OS=Homo sapiens OX=9606 GN=PIGR PE=1 SV=4”
[15] “sp|P0DUB6|AMY1A_HUMAN Alpha-amylase 1A OS=Homo sapiens OX=9606 GN=AMY1A PE=1 SV=1;sp|P0DTE8|AMY1C_HUMAN Alpha-amylase 1C OS=Homo sapiens OX=9606 GN=AMY1C PE=1 SV=1;sp|P0DTE7|AMY1B_HUMAN Alpha-amylase 1B OS=Homo sapiens OX=9606 GN=AMY1B PE=1 SV=1;sp|P19961|” [16] “sp|P12273|PIP_HUMAN Prolactin-inducible protein OS=Homo sapiens OX=9606 GN=PIP PE=1 SV=1”

6.4 Fasta Headers - Sample a4

“n [1]”tr|A0A139W9V5|A0A139W9V5_TRICA Histone H4 OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034951 PE=3 SV=1;tr|A0A139W9W1|A0A139W9W1_TRICA Histone H4 OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034951 PE=3 SV=1;sp|P62805|H4_HUMAN Histone H4 OS=Homo sapiens OX=9” [2] “tr|A0A139WAN8|A0A139WAN8_TRICA Tropomyosin-1, isoforms 9A/A/B-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC031441 PE=3 SV=1;tr|A0A139WAL9|A0A139WAL9_TRICA Tropomyosin-1, isoforms 9A/A/B-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC0” [3] “tr|A0A139WAP6|A0A139WAP6_TRICA Tropomyosin-2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC031442 PE=3 SV=1”
[4] “tr|A0A139WAP9|A0A139WAP9_TRICA Tropomyosin-2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC011461 PE=3 SV=1”
[5] “tr|A0A139WDY2|A0A139WDY2_TRICA Myosin heavy chain, muscle-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034002 PE=3 SV=1;tr|A0A139WE98|A0A139WE98_TRICA Myosin heavy chain, muscle-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034002 PE” [6] “tr|A0A139WE70|A0A139WE70_TRICA Myosin heavy chain, muscle-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034001 PE=3 SV=1”
[7] “tr|A0A139WGR3|A0A139WGR3_TRICA Apolipophorins-like protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034740 PE=4 SV=1”
[8] “tr|A0A139WNX9|A0A139WNX9_TRICA Arginine kinase OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC030882 PE=2 SV=1”
[9] “tr|D2A2S3|D2A2S3_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC007015 PE=4 SV=1”
[10] “tr|D2A4R3|D2A4R3_TRICA ATP synthase subunit beta OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC015322 PE=3 SV=1”
[11] “tr|D6WF19|D6WF19_TRICA Actin-87E-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC003326 PE=3 SV=1”
[12] “tr|D6WMB3|D6WMB3_TRICA Larval cuticle protein 8-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC014500 PE=4 SV=1”
[13] “tr|D6WQ50|D6WQ50_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC009873 PE=4 SV=1”
[14] “tr|D6WRY0|D6WRY0_TRICA Cytochrome c oxidase subunit 4 OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC009512 PE=3 SV=1”
[15] “tr|D6WSI9|D6WSI9_TRICA ATP synthase subunit alpha OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC008728 PE=3 SV=1;sp|P25705|ATPA_HUMAN ATP synthase subunit alpha, mitochondrial OS=Homo sapiens OX=9606 GN=ATP5F1A PE=1 SV=1”
[16] “tr|D6WUQ7|D6WUQ7_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005377 PE=4 SV=2”
[17] “tr|D6WUQ8|D6WUQ8_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005376 PE=4 SV=1”
[18] “tr|D6WUQ9|D6WUQ9_TRICA Larval serum protein 1 gamma chain-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC006769 PE=4 SV=1”
[19] “tr|D6WZH8|D6WZH8_TRICA Calcium-transporting ATPase OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012671 PE=3 SV=1”
[20] “tr|D6WZP8|D6WZP8_TRICA Troponin C, isoform 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012704 PE=4 SV=1”
[21] “tr|D6X073|D6X073_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1;tr|A0A139WC75|A0A139WC75_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1”
[22] “sp|P01833|PIGR_HUMAN Polymeric immunoglobulin receptor OS=Homo sapiens OX=9606 GN=PIGR PE=1 SV=4”
[23] “sp|P0DUB6|AMY1A_HUMAN Alpha-amylase 1A OS=Homo sapiens OX=9606 GN=AMY1A PE=1 SV=1;sp|P0DTE8|AMY1C_HUMAN Alpha-amylase 1C OS=Homo sapiens OX=9606 GN=AMY1C PE=1 SV=1;sp|P0DTE7|AMY1B_HUMAN Alpha-amylase 1B OS=Homo sapiens OX=9606 GN=AMY1B PE=1 SV=1;sp|P19961|” [24] “sp|P12273|PIP_HUMAN Prolactin-inducible protein OS=Homo sapiens OX=9606 GN=PIP PE=1 SV=1”

6.5 Fasta Headers - Sample a5

“n [1]”tr|A0A139WAN8|A0A139WAN8_TRICA Tropomyosin-1, isoforms 9A/A/B-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC031441 PE=3 SV=1;tr|A0A139WAL9|A0A139WAL9_TRICA Tropomyosin-1, isoforms 9A/A/B-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC0” [2] “tr|A0A139WAP9|A0A139WAP9_TRICA Tropomyosin-2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC011461 PE=3 SV=1”
[3] “tr|A0A139WDY2|A0A139WDY2_TRICA Myosin heavy chain, muscle-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034002 PE=3 SV=1;tr|A0A139WE98|A0A139WE98_TRICA Myosin heavy chain, muscle-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034002 PE” [4] “tr|A0A139WE70|A0A139WE70_TRICA Myosin heavy chain, muscle-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034001 PE=3 SV=1”
[5] “tr|A0A139WGR3|A0A139WGR3_TRICA Apolipophorins-like protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034740 PE=4 SV=1”
[6] “tr|A0A139WIM0|A0A139WIM0_TRICA Probable methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC032736 PE=3 SV=1”
[7] “tr|A0A139WNV6|A0A139WNV6_TRICA Elongation factor 1-alpha 1-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC031771 PE=3 SV=1;tr|A0A7I2V3H3|A0A7I2V3H3_HUMAN Elongation factor 1-alpha OS=Homo sapiens OX=9606 GN=EEF1A1 PE=1 SV=1;tr|A0A7I2V659|A0A7I2V6” [8] “tr|A0A139WNX9|A0A139WNX9_TRICA Arginine kinase OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC030882 PE=2 SV=1”
[9] “tr|A0A139WP69|A0A139WP69_TRICA Filamin-A-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005186 PE=3 SV=1;tr|D6W7G0|D6W7G0_TRICA Filamin-A-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005186 PE=3 SV=2”
[10] “tr|D2A4R3|D2A4R3_TRICA ATP synthase subunit beta OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC015322 PE=3 SV=1”
[11] “tr|D2A663|D2A663_TRICA Malate dehydrogenase OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC015050 PE=3 SV=1”
[12] “tr|D6W6D2|D6W6D2_TRICA Fatty acid synthase-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC011522 PE=4 SV=1”
[13] “tr|D6W849|D6W849_TRICA Transketolase-like protein 2 OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC004789 PE=4 SV=1”
[14] “tr|D6WF19|D6WF19_TRICA Actin-87E-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC003326 PE=3 SV=1”
[15] “tr|D6WJX6|D6WJX6_TRICA Vitellogenin domain-containing protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC013741 PE=4 SV=1”
[16] “tr|D6WSI9|D6WSI9_TRICA ATP synthase subunit alpha OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC008728 PE=3 SV=1;sp|P25705|ATPA_HUMAN ATP synthase subunit alpha, mitochondrial OS=Homo sapiens OX=9606 GN=ATP5F1A PE=1 SV=1”
[17] “tr|D6WSV2|D6WSV2_TRICA Tubulin beta chain OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC009589 PE=3 SV=1;tr|Q5ST81|Q5ST81_HUMAN Tubulin beta chain OS=Homo sapiens OX=9606 GN=TUBB PE=1 SV=1;tr|Q5JP53|Q5JP53_HUMAN Tubulin beta chain OS=Homo sapiens OX=9606 GN=” [18] “tr|D6WUQ7|D6WUQ7_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005377 PE=4 SV=2”
[19] “tr|D6WUQ8|D6WUQ8_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005376 PE=4 SV=1”
[20] “tr|D6WUQ9|D6WUQ9_TRICA Larval serum protein 1 gamma chain-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC006769 PE=4 SV=1”
[21] “tr|D6WV03|D6WV03_TRICA Glyceraldehyde-3-phosphate dehydrogenase OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC006170 PE=3 SV=1”
[22] “tr|D6WW81|D6WW81_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005795 PE=4 SV=1”
[23] “tr|D6X009|D6X009_TRICA 2-phospho-D-glycerate hydro-lyase OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012754 PE=3 SV=1;tr|D6X018|D6X018_TRICA 2-phospho-D-glycerate hydro-lyase OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC011729 PE=3 SV=1;tr|D6X017|D6X017_TRI” [24] “tr|D6X073|D6X073_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1;tr|A0A139WC75|A0A139WC75_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1”
[25] “tr|D6X0M8|D6X0M8_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012178 PE=4 SV=1”
[26] “sp|Q71U36|TBA1A_HUMAN Tubulin alpha-1A chain OS=Homo sapiens OX=9606 GN=TUBA1A PE=1 SV=1;sp|Q6PEY2|TBA3E_HUMAN Tubulin alpha-3E chain OS=Homo sapiens OX=9606 GN=TUBA3E PE=1 SV=2;sp|P0DPH7|TBA3C_HUMAN Tubulin alpha-3C chain OS=Homo sapiens OX=9606 GN=TUBA3C” [27] “sp|P01833|PIGR_HUMAN Polymeric immunoglobulin receptor OS=Homo sapiens OX=9606 GN=PIGR PE=1 SV=4”
[28] “sp|P0DUB6|AMY1A_HUMAN Alpha-amylase 1A OS=Homo sapiens OX=9606 GN=AMY1A PE=1 SV=1;sp|P0DTE8|AMY1C_HUMAN Alpha-amylase 1C OS=Homo sapiens OX=9606 GN=AMY1C PE=1 SV=1;sp|P0DTE7|AMY1B_HUMAN Alpha-amylase 1B OS=Homo sapiens OX=9606 GN=AMY1B PE=1 SV=1;sp|P19961|” [29] “sp|P12273|PIP_HUMAN Prolactin-inducible protein OS=Homo sapiens OX=9606 GN=PIP PE=1 SV=1”

6.6 Fasta Headers - Sample a6

“n [1]”tr|A0A139W9V5|A0A139W9V5_TRICA Histone H4 OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034951 PE=3 SV=1;tr|A0A139W9W1|A0A139W9W1_TRICA Histone H4 OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034951 PE=3 SV=1;sp|P62805|H4_HUMAN Histone H4 OS=Homo sapiens OX=9” [2] “tr|A0A139WAN8|A0A139WAN8_TRICA Tropomyosin-1, isoforms 9A/A/B-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC031441 PE=3 SV=1;tr|A0A139WAL9|A0A139WAL9_TRICA Tropomyosin-1, isoforms 9A/A/B-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC0” [3] “tr|A0A139WAP9|A0A139WAP9_TRICA Tropomyosin-2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC011461 PE=3 SV=1”
[4] “tr|A0A139WDY2|A0A139WDY2_TRICA Myosin heavy chain, muscle-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034002 PE=3 SV=1;tr|A0A139WE98|A0A139WE98_TRICA Myosin heavy chain, muscle-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034002 PE” [5] “tr|A0A139WE70|A0A139WE70_TRICA Myosin heavy chain, muscle-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034001 PE=3 SV=1”
[6] “tr|A0A139WGR3|A0A139WGR3_TRICA Apolipophorins-like protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034740 PE=4 SV=1”
[7] “tr|A0A139WNX9|A0A139WNX9_TRICA Arginine kinase OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC030882 PE=2 SV=1”
[8] “tr|D2A2S3|D2A2S3_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC007015 PE=4 SV=1”
[9] “tr|D2A4R3|D2A4R3_TRICA ATP synthase subunit beta OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC015322 PE=3 SV=1”
[10] “tr|D6W849|D6W849_TRICA Transketolase-like protein 2 OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC004789 PE=4 SV=1”
[11] “tr|D6WF19|D6WF19_TRICA Actin-87E-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC003326 PE=3 SV=1”
[12] “tr|D6WMB3|D6WMB3_TRICA Larval cuticle protein 8-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC014500 PE=4 SV=1”
[13] “tr|D6WQ50|D6WQ50_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC009873 PE=4 SV=1”
[14] “tr|D6WRY0|D6WRY0_TRICA Cytochrome c oxidase subunit 4 OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC009512 PE=3 SV=1”
[15] “tr|D6WSI9|D6WSI9_TRICA ATP synthase subunit alpha OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC008728 PE=3 SV=1;sp|P25705|ATPA_HUMAN ATP synthase subunit alpha, mitochondrial OS=Homo sapiens OX=9606 GN=ATP5F1A PE=1 SV=1”
[16] “tr|D6WUQ7|D6WUQ7_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005377 PE=4 SV=2”
[17] “tr|D6WUQ8|D6WUQ8_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005376 PE=4 SV=1”
[18] “tr|D6WUQ9|D6WUQ9_TRICA Larval serum protein 1 gamma chain-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC006769 PE=4 SV=1”
[19] “tr|D6WZH8|D6WZH8_TRICA Calcium-transporting ATPase OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012671 PE=3 SV=1”
[20] “tr|D6X009|D6X009_TRICA 2-phospho-D-glycerate hydro-lyase OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012754 PE=3 SV=1;tr|D6X018|D6X018_TRICA 2-phospho-D-glycerate hydro-lyase OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC011729 PE=3 SV=1;tr|D6X017|D6X017_TRI” [21] “tr|D6X073|D6X073_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1;tr|A0A139WC75|A0A139WC75_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1”
[22] “sp|P01833|PIGR_HUMAN Polymeric immunoglobulin receptor OS=Homo sapiens OX=9606 GN=PIGR PE=1 SV=4”
[23] “sp|P0DUB6|AMY1A_HUMAN Alpha-amylase 1A OS=Homo sapiens OX=9606 GN=AMY1A PE=1 SV=1;sp|P0DTE8|AMY1C_HUMAN Alpha-amylase 1C OS=Homo sapiens OX=9606 GN=AMY1C PE=1 SV=1;sp|P0DTE7|AMY1B_HUMAN Alpha-amylase 1B OS=Homo sapiens OX=9606 GN=AMY1B PE=1 SV=1;sp|P19961|” [24] “sp|P12273|PIP_HUMAN Prolactin-inducible protein OS=Homo sapiens OX=9606 GN=PIP PE=1 SV=1”
[25] “sp|Q96DR5|BPIA2_HUMAN BPI fold-containing family A member 2 OS=Homo sapiens OX=9606 GN=BPIFA2 PE=1 SV=2”

6.7 Fasta Headers - Sample a7

“n [1]”tr|A0A139W9V5|A0A139W9V5_TRICA Histone H4 OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034951 PE=3 SV=1;tr|A0A139W9W1|A0A139W9W1_TRICA Histone H4 OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034951 PE=3 SV=1;sp|P62805|H4_HUMAN Histone H4 OS=Homo sapiens OX=9” [2] “tr|A0A139WAN8|A0A139WAN8_TRICA Tropomyosin-1, isoforms 9A/A/B-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC031441 PE=3 SV=1;tr|A0A139WAL9|A0A139WAL9_TRICA Tropomyosin-1, isoforms 9A/A/B-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC0” [3] “tr|A0A139WAP9|A0A139WAP9_TRICA Tropomyosin-2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC011461 PE=3 SV=1”
[4] “tr|A0A139WDY2|A0A139WDY2_TRICA Myosin heavy chain, muscle-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034002 PE=3 SV=1;tr|A0A139WE98|A0A139WE98_TRICA Myosin heavy chain, muscle-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034002 PE” [5] “tr|A0A139WE70|A0A139WE70_TRICA Myosin heavy chain, muscle-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034001 PE=3 SV=1”
[6] “tr|A0A139WHF4|A0A139WHF4_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC033228 PE=4 SV=1”
[7] “tr|D2A4R3|D2A4R3_TRICA ATP synthase subunit beta OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC015322 PE=3 SV=1”
[8] “tr|D6WF19|D6WF19_TRICA Actin-87E-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC003326 PE=3 SV=1”
[9] “tr|D6WMB3|D6WMB3_TRICA Larval cuticle protein 8-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC014500 PE=4 SV=1”
[10] “tr|D6WNL2|D6WNL2_TRICA ATP synthase subunit delta, mitochondrial-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC013931 PE=3 SV=1”
[11] “tr|D6WQ50|D6WQ50_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC009873 PE=4 SV=1”
[12] “tr|D6WRT5|D6WRT5_TRICA Pupal cuticle protein Edg-84A-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC010057 PE=4 SV=1;tr|D6WRT1|D6WRT1_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC010054 PE=4 SV=1”
[13] “tr|D6WUQ7|D6WUQ7_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005377 PE=4 SV=2”
[14] “tr|D6WUQ8|D6WUQ8_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005376 PE=4 SV=1”
[15] “tr|D6WUQ9|D6WUQ9_TRICA Larval serum protein 1 gamma chain-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC006769 PE=4 SV=1”
[16] “tr|D6X073|D6X073_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1;tr|A0A139WC75|A0A139WC75_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1”
[17] “tr|D6X0X9|D6X0X9_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012828 PE=4 SV=1”
[18] “tr|D7ELA3|D7ELA3_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC008553 PE=4 SV=1”
[19] “sp|P01833|PIGR_HUMAN Polymeric immunoglobulin receptor OS=Homo sapiens OX=9606 GN=PIGR PE=1 SV=4”
[20] “sp|P0DUB6|AMY1A_HUMAN Alpha-amylase 1A OS=Homo sapiens OX=9606 GN=AMY1A PE=1 SV=1;sp|P0DTE8|AMY1C_HUMAN Alpha-amylase 1C OS=Homo sapiens OX=9606 GN=AMY1C PE=1 SV=1;sp|P0DTE7|AMY1B_HUMAN Alpha-amylase 1B OS=Homo sapiens OX=9606 GN=AMY1B PE=1 SV=1;sp|P19961|” [21] “sp|P12273|PIP_HUMAN Prolactin-inducible protein OS=Homo sapiens OX=9606 GN=PIP PE=1 SV=1”

6.8 Fasta Headers - Sample b1

“n[1]”tr|A0A139WGR3|A0A139WGR3_TRICA Apolipophorins-like protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034740 PE=4 SV=1”
[2] “tr|A0A139WNX9|A0A139WNX9_TRICA Arginine kinase OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC030882 PE=2 SV=1”
[3] “tr|D6W849|D6W849_TRICA Transketolase-like protein 2 OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC004789 PE=4 SV=1”
[4] “tr|D6WF19|D6WF19_TRICA Actin-87E-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC003326 PE=3 SV=1”
[5] “tr|D6WJX6|D6WJX6_TRICA Vitellogenin domain-containing protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC013741 PE=4 SV=1”
[6] “tr|D6WUQ7|D6WUQ7_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005377 PE=4 SV=2”
[7] “tr|D6WUQ8|D6WUQ8_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005376 PE=4 SV=1”
[8] “tr|D6WUQ9|D6WUQ9_TRICA Larval serum protein 1 gamma chain-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC006769 PE=4 SV=1”
[9] “sp|P0DUB6|AMY1A_HUMAN Alpha-amylase 1A OS=Homo sapiens OX=9606 GN=AMY1A PE=1 SV=1;sp|P0DTE8|AMY1C_HUMAN Alpha-amylase 1C OS=Homo sapiens OX=9606 GN=AMY1C PE=1 SV=1;sp|P0DTE7|AMY1B_HUMAN Alpha-amylase 1B OS=Homo sapiens OX=9606 GN=AMY1B PE=1 SV=1;sp|P19961|”

6.9 Fasta Headers - Sample b2

“n[1]”tr|A0A139WAN8|A0A139WAN8_TRICA Tropomyosin-1, isoforms 9A/A/B-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC031441 PE=3 SV=1;tr|A0A139WAL9|A0A139WAL9_TRICA Tropomyosin-1, isoforms 9A/A/B-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC0” [2] “tr|A0A139WAP9|A0A139WAP9_TRICA Tropomyosin-2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC011461 PE=3 SV=1”
[3] “tr|D6WF19|D6WF19_TRICA Actin-87E-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC003326 PE=3 SV=1”
[4] “tr|D6WQ50|D6WQ50_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC009873 PE=4 SV=1”
[5] “tr|D6WUQ7|D6WUQ7_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005377 PE=4 SV=2”
[6] “tr|D6WUQ8|D6WUQ8_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005376 PE=4 SV=1”
[7] “tr|D6WUQ9|D6WUQ9_TRICA Larval serum protein 1 gamma chain-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC006769 PE=4 SV=1”
[8] “tr|D6X073|D6X073_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1;tr|A0A139WC75|A0A139WC75_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1”
[9] “sp|P0DUB6|AMY1A_HUMAN Alpha-amylase 1A OS=Homo sapiens OX=9606 GN=AMY1A PE=1 SV=1;sp|P0DTE8|AMY1C_HUMAN Alpha-amylase 1C OS=Homo sapiens OX=9606 GN=AMY1C PE=1 SV=1;sp|P0DTE7|AMY1B_HUMAN Alpha-amylase 1B OS=Homo sapiens OX=9606 GN=AMY1B PE=1 SV=1;sp|P19961|”

6.10 Fasta Headers - Sample b3

“n[1]”tr|A0A139WAN8|A0A139WAN8_TRICA Tropomyosin-1, isoforms 9A/A/B-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC031441 PE=3 SV=1;tr|A0A139WAL9|A0A139WAL9_TRICA Tropomyosin-1, isoforms 9A/A/B-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC0” [2] “tr|A0A139WAP9|A0A139WAP9_TRICA Tropomyosin-2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC011461 PE=3 SV=1”
[3] “tr|A0A139WDY2|A0A139WDY2_TRICA Myosin heavy chain, muscle-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034002 PE=3 SV=1;tr|A0A139WE98|A0A139WE98_TRICA Myosin heavy chain, muscle-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034002 PE” [4] “tr|A0A139WE70|A0A139WE70_TRICA Myosin heavy chain, muscle-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034001 PE=3 SV=1”
[5] “tr|D2A4R3|D2A4R3_TRICA ATP synthase subunit beta OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC015322 PE=3 SV=1”
[6] “tr|D6WF19|D6WF19_TRICA Actin-87E-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC003326 PE=3 SV=1”
[7] “tr|D6WUQ8|D6WUQ8_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005376 PE=4 SV=1”
[8] “tr|D6WUQ9|D6WUQ9_TRICA Larval serum protein 1 gamma chain-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC006769 PE=4 SV=1”
[9] “tr|D6X073|D6X073_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1;tr|A0A139WC75|A0A139WC75_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1”

6.11 Fasta Headers - Sample b4

“n [1]”tr|A0A139WGR3|A0A139WGR3_TRICA Apolipophorins-like protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034740 PE=4 SV=1”
[2] “tr|A0A139WNV6|A0A139WNV6_TRICA Elongation factor 1-alpha 1-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC031771 PE=3 SV=1;tr|A0A7I2V3H3|A0A7I2V3H3_HUMAN Elongation factor 1-alpha OS=Homo sapiens OX=9606 GN=EEF1A1 PE=1 SV=1;tr|A0A7I2V659|A0A7I2V6” [3] “tr|A0A139WNX9|A0A139WNX9_TRICA Arginine kinase OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC030882 PE=2 SV=1”
[4] “tr|D6W6D2|D6W6D2_TRICA Fatty acid synthase-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC011522 PE=4 SV=1”
[5] “tr|D6W849|D6W849_TRICA Transketolase-like protein 2 OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC004789 PE=4 SV=1”
[6] “tr|D6WF19|D6WF19_TRICA Actin-87E-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC003326 PE=3 SV=1”
[7] “tr|D6WUQ7|D6WUQ7_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005377 PE=4 SV=2”
[8] “tr|D6WUQ8|D6WUQ8_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005376 PE=4 SV=1”
[9] “tr|D6WUQ9|D6WUQ9_TRICA Larval serum protein 1 gamma chain-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC006769 PE=4 SV=1”
[10] “sp|P0DUB6|AMY1A_HUMAN Alpha-amylase 1A OS=Homo sapiens OX=9606 GN=AMY1A PE=1 SV=1;sp|P0DTE8|AMY1C_HUMAN Alpha-amylase 1C OS=Homo sapiens OX=9606 GN=AMY1C PE=1 SV=1;sp|P0DTE7|AMY1B_HUMAN Alpha-amylase 1B OS=Homo sapiens OX=9606 GN=AMY1B PE=1 SV=1;sp|P19961|”

6.12 Fasta Headers - Sample b5

“n [1]”tr|A0A139WAN8|A0A139WAN8_TRICA Tropomyosin-1, isoforms 9A/A/B-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC031441 PE=3 SV=1;tr|A0A139WAL9|A0A139WAL9_TRICA Tropomyosin-1, isoforms 9A/A/B-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC0” [2] “tr|A0A139WAP9|A0A139WAP9_TRICA Tropomyosin-2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC011461 PE=3 SV=1”
[3] “tr|A0A139WDY2|A0A139WDY2_TRICA Myosin heavy chain, muscle-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034002 PE=3 SV=1;tr|A0A139WE98|A0A139WE98_TRICA Myosin heavy chain, muscle-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034002 PE” [4] “tr|A0A139WE70|A0A139WE70_TRICA Myosin heavy chain, muscle-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034001 PE=3 SV=1”
[5] “tr|A0A139WGR3|A0A139WGR3_TRICA Apolipophorins-like protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC034740 PE=4 SV=1”
[6] “tr|D2A2S3|D2A2S3_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC007015 PE=4 SV=1”
[7] “tr|D2A4R3|D2A4R3_TRICA ATP synthase subunit beta OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC015322 PE=3 SV=1”
[8] “tr|D6WF19|D6WF19_TRICA Actin-87E-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC003326 PE=3 SV=1”
[9] “tr|D6WUQ7|D6WUQ7_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005377 PE=4 SV=2”
[10] “tr|D6WUQ8|D6WUQ8_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005376 PE=4 SV=1”
[11] “tr|D6WUQ9|D6WUQ9_TRICA Larval serum protein 1 gamma chain-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC006769 PE=4 SV=1”
[12] “tr|D6X073|D6X073_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1;tr|A0A139WC75|A0A139WC75_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1”
[13] “sp|P0DUB6|AMY1A_HUMAN Alpha-amylase 1A OS=Homo sapiens OX=9606 GN=AMY1A PE=1 SV=1;sp|P0DTE8|AMY1C_HUMAN Alpha-amylase 1C OS=Homo sapiens OX=9606 GN=AMY1C PE=1 SV=1;sp|P0DTE7|AMY1B_HUMAN Alpha-amylase 1B OS=Homo sapiens OX=9606 GN=AMY1B PE=1 SV=1;sp|P19961|”

6.13 Fasta Headers - Sample b6

“n[1]”tr|D6WNL2|D6WNL2_TRICA ATP synthase subunit delta, mitochondrial-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC013931 PE=3 SV=1”
[2] “tr|D6WQ50|D6WQ50_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC009873 PE=4 SV=1”
[3] “tr|D6X073|D6X073_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1;tr|A0A139WC75|A0A139WC75_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1” [4] “tr|D7ELA3|D7ELA3_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC008553 PE=4 SV=1”

6.14 Fasta Headers - Sample b7

“n[1]”tr|D1ZZT6|D1ZZT6_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC007402 PE=4 SV=1”
[2] “tr|D6WF19|D6WF19_TRICA Actin-87E-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC003326 PE=3 SV=1”
[3] “tr|D6WI67|D6WI67_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC003599 PE=4 SV=1;tr|D6WI66|D6WI66_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC002841 PE=4 SV=1”
[4] “tr|D6WUQ8|D6WUQ8_TRICA Larval serum protein 2-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC005376 PE=4 SV=1”
[5] “tr|D6WUQ9|D6WUQ9_TRICA Larval serum protein 1 gamma chain-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC006769 PE=4 SV=1”
[6] “tr|D6X073|D6X073_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1;tr|A0A139WC75|A0A139WC75_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC012207 PE=4 SV=1”
[7] “tr|D7ELA3|D7ELA3_TRICA Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC008553 PE=4 SV=1”
[8] “sp|P0DUB6|AMY1A_HUMAN Alpha-amylase 1A OS=Homo sapiens OX=9606 GN=AMY1A PE=1 SV=1;sp|P0DTE8|AMY1C_HUMAN Alpha-amylase 1C OS=Homo sapiens OX=9606 GN=AMY1C PE=1 SV=1;sp|P0DTE7|AMY1B_HUMAN Alpha-amylase 1B OS=Homo sapiens OX=9606 GN=AMY1B PE=1 SV=1;sp|P19961|”

7 Used time

## [1] "Time used for analysis: 0.33 minutes"